User: user230613

gravatar for user230613
user230613280
Reputation:
280
Status:
Trusted
Location:
Europe
Last seen:
2 days, 1 hour ago
Joined:
5 years, 9 months ago
Email:
i********@hotmail.com

Posts by user230613

<prev • 64 results • page 1 of 7 • next >
0
votes
0
answers
118
views
0
answers
Comment: C: convert CDS coordinates of a GTF to amino acid coordinates respect the resultant
... Hi! Sorry if I didn't explain it clearly. In a nutshell, what I need is "simply" to extract the amino acid sequence corresponding to exon 2 and exon 3 of a given gene. And what I have, is a fasta file with the gene sequence, another fasta file with the protein sequence, and a GTF with the annotation ...
written 9 days ago by user230613280
1
vote
0
answers
118
views
0
answers
convert CDS coordinates of a GTF to amino acid coordinates respect the resultant protein
... Hello! I wonder if there is a way to convert CDS coordinates of a gene, to amino acid based coordinates , see the example: five_prime_utr1 1 495 exon1 496 568 CDS1 496 568 intron1 569 698 exon2 699 968 CDS2 699 968 The protein for this given gene, will start at 496 nucleoti ...
protein coordinates written 11 days ago by user230613280
0
votes
2
answers
6.7k
views
2
answers
Comment: C: Difference between the Fasta files from UCSC and Gencode/Ensembl
... Hello Denise, According to you answer, can I use then as reference genome the one located here: `ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz` ; and use the annotation files pr ...
written 2.4 years ago by user230613280
0
votes
1
answer
896
views
1
answer
Mate negative strand flag does not match read negative strand flag of mate
... I get this error when running **picard ValidateSamFile** in a RNA-Seq bam file produced by **hisat2**: ERROR: Record 52, Read name K00103:277:HL7HMBBXX:6:2109:23551:26054, Mate negative strand flag does not match read negative strand flag of mate This is the read in the bam file: `samtools v ...
rnaseq bam validatesamfile written 2.6 years ago by user230613280 • updated 2.6 years ago by Santosh Anand5.1k
0
votes
2
answers
4.0k
views
2
answers
Comment: C: TPM VS FPKM VS TMM and K-mer specific expression quantification
... Hello, again, I wonder if you could guide a little bit with my previous question? Thank you :) ...
written 2.7 years ago by user230613280
0
votes
2
answers
4.0k
views
2
answers
Comment: C: TPM VS FPKM VS TMM and K-mer specific expression quantification
... Hi Rob. Could you guide me a bit? If I want to find the expression of a given kmer (10nt) that is common between two transcripts, should I add the TPMs of both transcripts? ...
written 2.8 years ago by user230613280
3
votes
1
answer
1.7k
views
1
answer
GATK; Variant calling RNA-Seq best practices: bam processing steps
... Hi folks, I have been looking for the best approach for call the variants in RNA-Seq data. GATK proposes the following workflow: > 1) Map the reads using STAR. > > 2) Remove duplicates > > 3) Split N Trim > > 4) Indel realignment > > 5) Base recalibration > & ...
gatk variant_calling rna-seq written 2.9 years ago by user230613280 • updated 2.9 years ago by andrew.j.skelton736.0k
0
votes
2
answers
876
views
2
answers
Comment: C: Specific sequence abundance using RNA-Seq
... @Brian, I want to measure the expression of that sequence using RNA-Seq data, I don't want to extract the Kmer sequence from my reads. ...
written 3.1 years ago by user230613280
3
votes
2
answers
876
views
2
answers
Specific sequence abundance using RNA-Seq
... Hi, I would like to measure the expression, the abundance, of a given sequence, a specific 9-mer. I have `RNA-Seq` data. I know that the 9-mer is not unique in the genome, is not private of a specific gene. It is present in more than one isoform of gene A and also is present in gene B. How can I ge ...
expression rna-seq written 3.1 years ago by user230613280 • updated 3.1 years ago by Brian Bushnell17k
0
votes
7
answers
17k
views
7
answers
Comment: C: What Ngs Read Simulators Are Available For Paired-End Data?
... Thank you for the fast answer. I'll try the bedtools pre-step. Another issue.. I've realised that in PE mode, the names of the output reads in the two files are not paired, is there any option for this? ...
written 3.1 years ago by user230613280

Latest awards to user230613

Popular Question 7 days ago, created a question with more than 1,000 views. For promoter position estimation
Great Question 21 months ago, created a question with more than 5,000 views. For Intersect multiple bed and keep all fields
Popular Question 21 months ago, created a question with more than 1,000 views. For Samtools: variant calling for INDELs
Popular Question 21 months ago, created a question with more than 1,000 views. For promoter position estimation
Popular Question 21 months ago, created a question with more than 1,000 views. For ggheatmap R script error.
Popular Question 21 months ago, created a question with more than 1,000 views. For consensus sequence of complex estructural variants
Popular Question 21 months ago, created a question with more than 1,000 views. For CIRCOS plot with Chip-Seq Data
Popular Question 21 months ago, created a question with more than 1,000 views. For Does vcf-consensus support indels?
Popular Question 21 months ago, created a question with more than 1,000 views. For Intersect multiple bed and keep all fields
Popular Question 21 months ago, created a question with more than 1,000 views. For Samtools: variant calling for INDELs
Great Question 2.3 years ago, created a question with more than 5,000 views. For Trinity strand specific: RF or FR
Great Question 2.3 years ago, created a question with more than 5,000 views. For Extract reads within given region, and their mates
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Samtools: variant calling for INDELs
Popular Question 2.3 years ago, created a question with more than 1,000 views. For promoter position estimation
Popular Question 2.3 years ago, created a question with more than 1,000 views. For ggheatmap R script error.
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Intersect multiple bed and keep all fields
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Samtools: variant calling for INDELs
Popular Question 2.4 years ago, created a question with more than 1,000 views. For promoter position estimation
Popular Question 2.6 years ago, created a question with more than 1,000 views. For promoter position estimation
Popular Question 2.6 years ago, created a question with more than 1,000 views. For CIRCOS plot with Chip-Seq Data
Popular Question 2.8 years ago, created a question with more than 1,000 views. For promoter position estimation
Popular Question 3.1 years ago, created a question with more than 1,000 views. For promoter position estimation
Popular Question 3.1 years ago, created a question with more than 1,000 views. For CIRCOS plot with Chip-Seq Data
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Intersect multiple bed and keep all fields
Student 3.3 years ago, asked a question with at least 3 up-votes. For Extract reads within given region, and their mates

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1658 users visited in the last hour